Predicting residue-wise contact orders in proteins by support vector regression

Background The residue-wise contact order (RWCO) describes the sequence separations between the residues of interest and its contacting residues in a protein sequence. It is a new kind of one-dimensional protein structure that represents the extent of long-range contacts and is considered as a generalization of contact order. Together with secondary structure, accessible surface area, the B factor, and contact number, RWCO provides comprehensive and indispensable important information to reconstructing the protein three-dimensional structure from a set of one-dimensional structural properties. Accurately predicting RWCO values could have many important applications in protein three-dimensional structure prediction and protein folding rate prediction, and give deep insights into protein sequence-structure relationships. Results We developed a novel approach to predict residue-wise contact order values in proteins based on support vector regression (SVR), starting from primary amino acid sequences. We explored seven different sequence encoding schemes to examine their effects on the prediction performance, including local sequence in the form of PSI-BLAST profiles, local sequence plus amino acid composition, local sequence plus molecular weight, local sequence plus secondary structure predicted by PSIPRED, local sequence plus molecular weight and amino acid composition, local sequence plus molecular weight and predicted secondary structure, and local sequence plus molecular weight, amino acid composition and predicted secondary structure. When using local sequences with multiple sequence alignments in the form of PSI-BLAST profiles, we could predict the RWCO distribution with a Pearson correlation coefficient (CC) between the predicted and observed RWCO values of 0.55, and root mean square error (RMSE) of 0.82, based on a well-defined dataset with 680 protein sequences. Moreover, by incorporating global features such as molecular weight and amino acid composition we could further improve the prediction performance with the CC to 0.57 and an RMSE of 0.79. In addition, combining the predicted secondary structure by PSIPRED was found to significantly improve the prediction performance and could yield the best prediction accuracy with a CC of 0.60 and RMSE of 0.78, which provided at least comparable performance compared with the other existing methods. Conclusion The SVR method shows a prediction performance competitive with or at least comparable to the previously developed linear regression-based methods for predicting RWCO values. In contrast to support vector classification (SVC), SVR is very good at estimating the raw value profiles of the samples. The successful application of the SVR approach in this study reinforces the fact that support vector regression is a powerful tool in extracting the protein sequence-structure relationship and in estimating the protein structural profiles from amino acid sequences.

SwarmPS: Rapid, semi-automated single particle selection software

Single particle analysis (SPA) coupled with high-resolution electron cryo-microscopy is emerging as a powerful technique for the structure determination of membrane protein complexes and soluble macromolecular assemblies. Current estimates suggest that ∼104–105 particle projections are required to attain a 3 Å resolution 3D reconstruction (symmetry dependent). Selecting this number of molecular projections differing in size, shape and symmetry is a rate-limiting step for the automation of 3D image reconstruction. Here, we present SwarmPS, a feature rich GUI based software package to manage large scale, semi-automated particle picking projects. The software provides cross-correlation and edge-detection algorithms. Algorithm-specific parameters are transparently and automatically determined through user interaction with the image, rather than by trial and error. Other features include multiple image handling (∼102), local and global particle selection options, interactive image freezing, automatic particle centering, and full manual override to correct false positives and negatives. SwarmPS is user friendly, flexible, extensible, fast, and capable of exporting boxed out projection images, or particle coordinates, compatible with downstream image processing suites.

Corporate governance, accounting and finance: a review

We review accounting and finance research on corporate governance (CG). In the course of our review, we focus on a particularly vexing issue, namely endogeneity in the relationships between CG and other matters of concern to accounting and finance scholars, and suggest ways to deal with it. Given the advent of large commercial CG databases, we also stress the importance of how CG is measured and in particular, the construction of CG indices, which should be sensitive to local institutional arrangements, and the need to capture both internal and external aspects of governance. The ‘stickiness’ of CG characteristics provides an additional challenge to CG scholars. Better theory is required, for example, to explain whether various CG practices substitute for each other or are complements. While a multidisciplinary approach to developing better theory is never without its difficulties, it could enrich the current body of knowledge in CG. Despite the vastness of the existing CG literature, these issues do suggest a number of avenues for future research.

Designing university, government and industry community engagement to build informed and effective interventions in the area of road safety

Individuals, community organisations and industry have always been involved to varying degrees in efforts to address the Queensland road toll. Traditionally, road crash prevention efforts have been led by state and local government organisations. While community and industry groups have sometimes become involved (e.g. Driver Reviver campaign), their efforts have largely been uncoordinated and under-resourced. A common strength of these initiatives lies in the energy, enthusiasm and persistence of community-based efforts. Conversely, a weakness has sometimes been the lack of knowledge, awareness or prioritisation of evidence-based interventions or their capacity to build on collaborative efforts. In 2000, the Queensland University of Technology’s Centre for Accident Research and Road Safety – Queensland (CARRS-Q) identified this issue as an opportunity to bridge practice and research and began acknowledging a selection of these initiatives, in partnership with the RACQ, through the Queensland Road Safety Awards program. After nine years it became apparent there was need to strengthen this connection, with the Centre establishing a Community Engagement Workshop in 2009 as part of the overall Awards program. With an aim of providing community participants opportunities to see, hear and discuss the experiences of others, this event was further developed in 2010, and with the collaboration of the Queensland Department of Transport and Main Roads, the RACQ, Queensland Police Service and Leighton Contractors Pty Ltd, a stand-alone Queensland Road Safety Awards Community Engagement Workshop was held in 2010. Each collaborating organisation recognised a need to mobilise the community through effective information and knowledge sharing, and recognised that learning and discussion can influence lasting behaviour change and action in this often emotive, yet not always evidence-based, area. This free event featured a number of speakers representing successful projects from around Australia and overseas. Attendees were encouraged to interact with the speakers, to ask questions, and most importantly, build connections with other attendees to build a ‘community road safety army’ all working throughout Australia on projects underpinned by evaluated research. The workshop facilitated the integration of research, policy and grass-roots action enhancing the success of community road safety initiatives. For collaboration partners, the event enabled them to transfer their knowledge in an engaged approach, working within a more personal communication process. An analysis of the success factors for this event identified openness to community groups and individuals, relevance of content to local initiatives, generous support with the provision of online materials and ongoing communication with key staff members as critical and supports the view that the university can directly provide both the leadership and the research needed for effective and credible community-based initiatives to address injury and death on the roads.

From margins to mainstream : how screen and creative industries developed in the Northern Rivers region of NSW : 2000–2010

This thesis explores the proposition that growth and development in the screen and creative industries is not confined to the major capital cities. Lifestyle considerations, combined with advances in digital technology, convergence and greater access to broadband are altering requirements for geographic location, and creative workers are being drawn away from the big metropolises to certain regional areas. Regional screen industry enclaves are emerging outside of London, in the Highlands and Islands of Scotland, in Nova Scotia in Canada and in New Zealand. In the Australian context, the proposition is tested in an area regarded as a ‘special case’ in creative industry expansion: the Northern Rivers region of NSW. A key feature of the ‘specialness’ of this region is the large number of experienced, credited producers who live and operate their businesses within the region. The development of screen and creative industries in the Northern Rivers over the decade 2000 – 2010 has implications for regional regeneration and offers new insights into the rapidly changing screen industry landscape. This development also has implications for creative industry discourse, especially the dominance of the urban in creative industries thought. The research is pioneering in a number of ways. Building on the work conducted for my Masters thesis in 2000, a second study was conducted during the research phase, adapting creative industries theory and mapping methods, which have been largely city and nation-centric, and applying them to a regional context. The study adopted an action research approach as an industry development strategy for screen industries, while at the same time developing fine-grained ground up methods for collecting primary quantitative data on the size and scope of the creative industries. In accordance with the action research framework, the researcher also acted in the dual roles of industry activist and screen industry producer in the region. The central focus of the research has been both to document and contribute to the growth and development of screen and creative industries over the past decade in the Northern Rivers region. These interventions, along with policy developments at both a local and national level, and broader global shifts, have had the effect of repositioning the sector from a marginal one to a priority area considered integral to the future economic and cultural life of the region. The research includes a detailed mapping study undertaken in 2005 with comparisons to an earlier 2000 study and to ABS data for 2001 and 2006 to reveal growth trends. It also includes two case studies of projects that developed from idea to production and completion in the region during the decade in question. The studies reveal the drivers, impediments and policy implications for sustaining the development of screen industries in a regional area. A major finding of the research was the large and increasing number of experienced producers who operate within the region and the leadership role they play in driving the development of the emerging local industry. The two case studies demonstrate the impact of policy decisions on local screen industry producers and their enterprises. A brief overview of research in other regional areas is presented, including two international examples, and what they reveal about regional regeneration. Implications are drawn for creative industries discourse and regional development policy challenges for the future.

An epistemic community as influencer and implementer in local government accounting in Australia

This paper adopts an epistemic community framework to explicate the dual role of epistemic communities as influencers of accounting policy within regulatory space and as implementers who effect change within the domain of accounting. The context is the adoption and implementation of fair value accounting within local government in New South Wales (NSW). The roles and functions of Australian local government are extensive, and include the development and maintenance of infrastructure, provision of recreational facilities, certain health and community services, buildings, cultural facilities, and in some cases, water and sewerage (Australian Local Government Association, 2009). The NSW state Department of Local Government (DLG) is responsible for legislation and policy development to ensure that local councils are able to deliver ‘quality services to their communities in a sustainable manner’ (DLG, 2008c). These local councils receive revenue from various sources including property rates, government grants and user-pays service provision. In July 2006 the DLG issued Circular 06-453 to councils (DLG, 2006c), mandating the staged adoption of fair value measurement of infrastructure assets. This directive followed the policy of NSW State Treasury (NSW Treasury, 2007),4 and an independent inquiry into the financial sustainability of local councils (LGSA, 2006). It was an attempt to resolve the inconsistency in public sector asset valuation in NSW Local Governments, and to provide greater usefulness and comparability of financial statements.5 The focus of this study is the mobilization of accounting change by the DLG within this wider political context. When a regulatory problem arises, those with political power seek advice from professionals with relevant skill and expertise (Potter, 2005). This paper explores the way in which professionals diffuse accounting ‘problems’ and the associated accounting solutions ‘across time and space’ (Potter, 2005, p. 277). The DLG’s fair value accounting policy emanated from a ‘regulatory space’ (Hancher and Moran, 1989)6 as a result of negotiations between many parties, including accounting and finance professionals. Operating within the local government sector, these professionals were identified by the DLG as being capable of providing helpful input. They were also responsible for the implementation of the new olicy within local councils. Accordingly they have been dentified as an pistemic community with the ability to ranslate regulatory power by changing he domain of ccounting (Potter, 2005, p. 278).7 The paper is organised as follows. The background to the LG’s decision to require the introduction of fair value accounting for infrastructure assets is explored. Following this, the method of the study is described, and the epistemic community framework outlined. In the next sections, evidence of the influencing and implementing roles of epistemic groups is provided. Finally, conclusions are drawn about the significance of these groups both within regulatory space in developing accounting regulation, and in embedding change within the domain of accounting.

Drinking and driving in Vietnam : perceptions and risk

Road traffic injuries are a major global public health problem but continue to receive inadequate attention. Alcohol influences both risk and consequence of road traffic injury but the scale of the problem is not well understood in many countries. In Vietnam, economic development has brought a substantial increase in the number of registered motorcycles as well as alcohol consumption. Traffic injury is among the leading causes of death in Vietnam but there is little local information regarding alcohol related traffic injuries. The primary goal of this study is to explore the drinking and driving patterns of males and their perceptions towards drink-driving and to determine the relationship between alcohol consumption and road traffic injuries. Furthermore, this thesis aims to present the situation analysis for choosing priority actions to reduce drinking and driving in Vietnam. The study is a combination of two cross-sectional surveys and a pilot study. The pilot study, involving 224 traffic injured patients, was conducted to test the tools and the feasibility of approach methods. In the first survey, male patrons (n=464) were randomly selected at seven restaurants. Face-to-face interviews were conducted when patrons just arrived and breath tests were collected when they were about to leave the restaurant. In the second survey, male patients admitted to hospital following a traffic injury (n=480, of which 414 were motorcycle or bicycle riders) were interviewed and their blood alcohol concentration (BAC) measured by breathalyzer. The results show broadly similar patterns of drinking and driving among male patrons and male traffic injured patients with a high frequency of drinking and drink-driving reported among the majority of the two groups. A high proportion of male patrons were leaving restaurants with a BAC over the legal limit. Factors that significantly associate with the number of drinks and BAC were age, hazardous drinking, frequency of drink-driving in the past year, self-estimated number of drinks consumed to drive legally, perceived family’s disapproval of drink-driving, and perceived legal risk and physical risk. The proportion of patrons and patients with BAC above the legal limit of 0.05 were 86.7% and 60.4% respectively, which was much higher than found in previous studies. In addition, both groups had a high prevalence of BAC over 0.15g/100ml (39.7% of patrons and 45.6% patients), a level that can seriously affect driving capacity. Results from the case-crossover analysis for patients indicate a dose-response relationship between alcohol consumption and the risk of traffic injury. The risk of traffic injury increased when alcohol was consumed before driving and there was a more than 13 fold increase when six or more drinks were consumed. Regarding perceptions towards drinking and driving, findings corroborate the low awareness among males in Vietnam, with a majority of respondents holding a low knowledge of safe and legally permissible alcohol use, and a low perceived risk of drinking and driving. The results also indicate a huge gap in prevention skills in terms of planning ahead or using alternative transport to avoid drink-driving and a perception by patrons and patients of a low rate of disapproval of drink-driving from peers and family. Findings in this study have considerable implications for national policy, injury prevention, clinical practice, reporting systems, and for further research. The low rate of compliance with existing laws and a generally low perceived legal risk toward drink-driving in this study call for the strengthening of enforcement along with mass media campaigns and news coverage in order to decrease the widespread perception of impunity and thereby, to reduce the level of drink-driving. In addition, no significant difference was found in this study on risk of traffic injuries between car drivers and motorcycle drivers. The current inconsistency between legal BAC for drivers of motorcycles, compared to cars, thus needs addressing. Furthermore, as drinking was found to be very common, rather than solely targeting drink-driving, it is important to call for a more strategic and comprehensive approach to alcohol policy in Viet Nam. This study also has considerable implications for clinical practice in terms of screening and brief interventions. Our study suggests that the short form of the AUDIT (AUDIT-C) screening tool is appropriate for use in busy emergency departments. The high proportion of traffic injured patients with evidence of alcohol abuse or hazardous drinking suggests that brief interventions by alcohol and drug counselors in emergency departments are a sensible option to addressing this important problem. The significance of this study is in the combination of the systematic collection of breath test and use of case-crossover design to estimate the risk of traffic injuries after alcohol consumption. The results provide convincing evidence to policy makers, health authorities and the media to help raise community awareness and policy advocacy toward the drinkdriving problem in Vietnam. The findings suggest an urgent need for a multi-sectoral approach to curtail drink-driving in Vietnam, especially programs to raise community awareness and effective legal enforcement. Furthermore, serving as a situation analysis, the thesis should inform the formulation of interventions designed to curtail drinking and driving in Vietnam and other developing countries.

Knowledge and attitudes of paediatric nurses related to breastfeeding

Introduction: Almost 90% of Australian mothers are exclusively breastfeeding when they discharge from maternity hospitals but by six months of age breastfeeding infants have reduced to 32% nationally and 19% in Queensland, far below the national target of 80%. Many factors influence the choice to breastfeed, including health care provision, therefore the knowledge and attitudes of paediatric nurses have the potential to affect breastfeeding duration. Aims: To assess current breastfeeding knowledge and attitudes of paediatric nurses in metropolitan and regional Queensland settings. Method: The study used a cross-sectional survey design. The tool was developed from several documented health professional questionnaires about breastfeeding, with permission from authors. Survey items relating breastfeeding physiology, factors relating to breastfeeding success, and local, national and international policies were also included. Ethics approval was granted from the appropriate Ethics Committees to conduct the survey through tertiary metropolitan and regional hospital settings. Results: A total of 241 surveys were returned, achieving a response rate of 53%. Nurses acknowledged breastmilk as the best source of nutrition for infants (99%, n=238) and that mothers should be encouraged to breastfeed (92%, n=221). However, many respondents considered infant formula a nutritional equivalent (44%, n=105) and (47%, n=113) were unaware that supplemental formulas interfered with successful breastfeeding. Most nurses recognised that stress (e.g. infant hospitalisation) impacts on the success of breastfeeding (90%, n=216). Knowledge of breastfeeding anatomy and physiology was poor and a substantial number of nurses did not identify correct attachment in response to two diagrammatic representations (76%, n=183 and 45%, n=109). Survey results demonstrated deficiencies in knowledge that would impact on support provided to breastfeeding mothers. Knowledge deficits were also identified relating to local, national and international policies and protocols concerning breastfeeding and breastmilk substitutes. Conclusion: Breastfeeding knowledge and attitudes were exceptional in areas related to general breastfeeding knowledge. However, in areas directly related to nursing practice, considerable deficits in paediatric nurses' knowledge and attitudes were identified. Lack of appropriate skills, knowledge and varying attitudes amongst paediatric nurses has the potential to negatively impact on the education, advice and support provided to breastfeeding mothers and their families whilst their infant is in hospital. These study findings will guide future research and strategies to improve knowledge and policy statements to assist paediatric nurses in fulfilling their role.

HR practices and challenges in Chinese firms : comparison with Western firms

This research compares Chinese HRM with Western HRM, particularly in the areas of development of HR information systems (HRIS) and HR measurement systems and their relation to HR’s involvement as a strategic partner in firms. The research uses a 3-stage model of HRIS (workforce profiling, business insight, and strategic driver) based on studies of Irmer and Ellerby (2005) and Boudreau and Ramstad (2003) to compare the relative stages of development of Chinese and Western HRM. The quantitative aspect of the study comprises a survey of senior HR practitioners from 171 Chinese firms whose data is compared with data from Irmer and Ellerby’s study of Australian and U.S. HRM (2005) and Lawler et al’s series of studies of U.S firms (1995, 1998, 2001, 2004). The main results of the comparison are that Chinese HRM generally lags behind Western HRM. In particular, Chinese HR professionals allocate less time to strategic activities and their roles are less strategic than those of Western HR professionals. The HR measurement systems of Chinese firms are more limited in function, and the HR information systems of Chinese companies are less automated and integrated. However there is also evidence of a “two speed” HR system in China with a small proportion of firms having highly sophisticated HR systems but with a much larger proportion of Chinese firms than in the West having only the most basic HR information systems. This ‘two speed” system is in part attributable to a split between the relatively advanced HR systems of large State Owned Enterprises and the basic systems that predominate in smaller, growing Local Private firms. The survey study is complemented by a series of interviews with a number of senior Chinese HR practitioners who provide richer insights into their experiences and the challenges they face in contemporary Chinese firms.

Online geographic information systems for improving health planning practice : lessons learned from the case study of Logan-Beaudesert, Australia

This study examines the impact of utilising a Decision Support System (DSS) in a practical health planning study. Specifically, it presents a real-world case of a community-based initiative aiming to improve overall public health outcomes. Previous studies have emphasised that because of a lack of effective information, systems and an absence of frameworks for making informed decisions in health planning, it has become imperative to develop innovative approaches and methods in health planning practice. Online Geographical Information Systems (GIS) has been suggested as one of the innovative methods that will inform decision-makers and improve the overall health planning process. However, a number of gaps in knowledge have been identified within health planning practice: lack of methods to develop these tools in a collaborative manner; lack of capacity to use the GIS application among health decision-makers perspectives, and lack of understanding about the potential impact of such systems on users. This study addresses the abovementioned gaps and introduces an online GIS-based Health Decision Support System (HDSS), which has been developed to improve collaborative health planning in the Logan-Beaudesert region of Queensland, Australia. The study demonstrates a participatory and iterative approach undertaken to design and develop the HDSS. It then explores the perceived user satisfaction and impact of the tool on a selected group of health decision makers. Finally, it illustrates how decision-making processes have changed since its implementation. The overall findings suggest that the online GIS-based HDSS is an effective tool, which has the potential to play an important role in the future in terms of improving local community health planning practice. However, the findings also indicate that decision-making processes are not merely informed by using the HDSS tool. Instead, they seem to enhance the overall sense of collaboration in health planning practice. Thus, to support the Healthy Cities approach, communities will need to encourage decision-making based on the use of evidence, participation and consensus, which subsequently transfers into informed actions.